More NEURON + Python documentation

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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ted
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More NEURON + Python documentation

Post by ted »

In addition to the instructions contained in the Programmer's Reference,
and whatever gems you might glean from these discussion threads, more
documentation is appearing that you might find helpful.

Andrew Davison has created a very nice set of instructions and examples for
using NEURON with Python.
http://www.davison.webfactional.com/not ... on-python/
shows how to install NEURON with Python for Linux using the bash shell.
http://www.davison.webfactional.com/not ... oc-python/
shows how to access hoc variables, procs, etc. from Python.
http://www.davison.webfactional.com/not ... on-python/
shows how to model single cells in NEURON with the Python interpreter.
PhilippRautenberg
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Re: More NEURON + Python documentation

Post by PhilippRautenberg »

Hello together,

I put also a pyNEURON tutorial online. See: http://neuro.paedia.info/

Many ideas and suggestions for this tutorial go back to the pyneuron workshop at the CNS in Berlin 2009. At this point I have to thank Alvaro, Andrew, Eilif, Michele, Robert, and many more people from the conference/workshop for fruitful discussions.

Cheers, Philipp
ted
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Re: More NEURON + Python documentation

Post by ted »

Excellent, Philipp!
Tom Close
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Re: More NEURON + Python documentation

Post by Tom Close »

I was just trying to find Philipp's pyNEURON tutorial again and found it has moved to http://www.paedia.info/index.html
romain.caze

Re: More NEURON + Python documentation

Post by romain.caze »

Hi All,

Thank you Tom for the new link as Philipp's tuto is great.
Here is a link to another NEURON + Python tutorial. https://romaincaze.wordpress.com/2015/0 ... -tutorial/

Cheers,
R.
mzenker
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Location: Germany

Re: More NEURON + Python documentation

Post by mzenker »

Almost all of the links (except Ramain's tutorial) are dead.
But I have found Andrew Davison's instructions here: http://andrewdavison.info/notes/
ramcdougal
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Location: Yale School of Public Health

Re: More NEURON + Python documentation

Post by ramcdougal »

Since this discussion, there had been a lot of work on the Python interface to make things cleaner, especially in NEURON 7.5 and 7.6.

We're in the process of reworking the main NEURON Python tutorial:

https://neuron.yale.edu/neuron/static/d ... index.html

The draft revised pages (only the first three parts of the tutorial so far) for now are downloadable as Jupyter notebooks from:

https://neuron.yale.edu/ftp/ramcdougal/ ... n-tutorial

Also note that since the above discussion, the programmer's reference now defaults to showing code and examples in Python:

https://www.neuron.yale.edu/neuron/stat ... index.html
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